Effects of genetic variations and altered gene expression patterns on severe malarial Anaemia pathogenesis in children from siaya county

Abstract

Malaria remains a significant health burden in sub-Saharan Africa. In holoendemic Plasmodium Falciparum transmission regions, such as western Kenya, children aged <5 years are vulnerable due to naïve malarial immunity. Among these children, severe malarial anaemia (SMA, haemoglobin (Hb)<5.0 g/dL) is the most prevalent and life-threatening manifestation of severe malaria. Despite its high burden, the molecular mechanism driving SMA pathogenesis, particularly the host genetic and transcriptomic factors as well as parasite gene expression, remains poorly defined. This study determined the effect of human genetic variation, as well as the host and P. falciparum gene expression patterns on SMA pathogenesis in children (<5 years) from Siaya County. The specific objectives included: to determine the relationship between genetic polymorphisms in natural cytotoxicity-triggering receptor (NCR3) (rs2736191:C>G and rs11575837:C>T) and longitudinal malaria outcomes; to determine the influence of NK cell networks, and other immune signalling pathways on the pathogenesis of paediatric SMA, and to profile the transcriptome of blood-stage P. falciparum in children with SMA. The selected NCR3 SNPs reduced NCR3 transcription, thereby impairing NK cell recognition of iRBCs and cytokine signaling. In contrast, host and parasite transcriptomics provide insights into their expression profiles in SMA. Genomic DNA from dried bloodspots collected at enrollment from 1,515 children was genotyped for the NCR3 variants using TaqMan® assays, while total RNA from 66 children was used for RNA sequencing via Illumina® sequencing. Poisson regression revealed that the rs11575837 TT genotype increased the risk of malaria episodes [Incidence Rate Ratio (IRR)=1.540, P=0.009], while the CC haplotype was protective against SMA (IRR=0.823, P=0.009). Host transcriptomics of RNA from whole-blood collected at enrollment from 66 children revealed 6,862 differentially expressed genes (DEGs) in SMA vs. non-SMA, with increased NK cell expression (P=0.002) and dysregulated Inflammation_NK cell cytotoxicity network (Padj=3.628E-04) in SMA. Furthermore, the HSP60-HSP70-TLR2/4 signalling pathway (Padj=5.483E-09) was among the most dysregulated immune pathways, with altered glutamine metabolism in SMA. P. falciparum transcriptomics from 60 children revealed 566 DEGs in SMA vs. non-SMA. Weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) of the DEGs identified parasite pathways potentially contributing to SMA. Additionally, the hub nodes in the WGCNA and PPI networks, which increased the risk of SMA, were identified. Overall, NCR3 variation influences malaria and SMA risk, while SMA is characterised by dysregulated NK-cell function, impaired HSP60-HSP70-TLR2/4 signalling, altered glutamine metabolism, and distinct parasite transcriptional profiles. These findings advance the understanding of SMA pathogenesis and identify hub nodes as potential therapeutic targets.